Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1150516 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30333103.fastq.gz | Fastqsanger.gz | |||
| SRR30333104.fastq.gz | Fastqsanger.gz | |||
| SRR30333105.fastq.gz | Fastqsanger.gz | |||
| SRR30333106.fastq.gz | Fastqsanger.gz | |||
| SRR30333107.fastq.gz | Fastqsanger.gz |
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Project description:The investigation of archaeological samples, which are of inestimable value, requires minimally destructive or non-destructive sampling techniques. One of the most promising and recent non-invasive techniques is known under the acronym EVA, an ethylene vinyl acetate film which avoids contamination and proteins damages. The present work reports the results of the metaproteomic analysis performed on the middle part of a trunk, and on the portion of a trunk tip tissue of two different woolly mammoths some 40000 years’ old. In particular, proteins were extracted by applying EVA (Ethylene-Vinyl Acetate) films to the surface of these tissues belonging to two Mammuthus primigenus specimens, discovered in two regions located in the Russian Far East, and then investigated via a shotgun MS-based approach. This approach allowed to obtain two interesting results: i) an indirect description of the habitat of these two mammoths, and ii) an improved sequence characterization of the alpha-1 type I collagen (col1a1), the major component of type I collagen. Sequence characterization of the col1a1 highlighted some differences between M. primigenius and other Proboscidea together with the identification of two potentially diagnostic amino acidic mutations that could be used to reliably distinguish the Mammuthus primigenius respect to the other two genera of elephantids (i.e. Elephas and Loxodonta), and the extinct American mastodon (i.e. Mammut americanum). The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones.
2022-05-19 | PXD029558 | Pride
Project description:Palaeoproteomic study of mummified human skin using a non-destructive sampling technique, based on mixed-bed chromatographic media stabilised on ethylene vinyl acetate membranes (“EVA”), which had previously been used exclusively on historical material, was successful in extracting ancient proteins from the surface of Ancient Egyptian mummies. We tested the method on a decontextualised fragment of skin and assessed the endogeneity of its metaproteome by comparison with a procedural blank. Furthermore, we retrieved and authenticated sequences of collagen and keratin from the mummy of a young woman (Supp. 16747 of the Museum of Anthropology and Ethnography of the University of Turin) who lived and died between 2400 and 2200 BC, during the Old Kingdom of Egypt.
2020-06-10 | PXD015572 | Pride
Project description:There is global concern regarding the fate and effects of microplastics in the environment, particularly in aquatic systems. In this study, ethylene acrylic acid copolymer particles were evaluated in a chronic toxicity study with the aquatic invertebrate, Daphnia magna. The study design included a natural particle control treatment (i.e., silica) in order to discern any potential physical effects of a particlefrom intrinsic toxicity of the test material. In addition to the standard endpoints of survival, growth, and reproduction, the transcriptomic profile of control and ethylene acrylic acid copolymer-exposed D. magna were evaluated at the termination of the 21-day toxicity study. No significant effects on D. magna growth, survival, or reproduction were observed in the study in comparison to both particle and untreated control groups. Significant transcriptomic alterations were induced in the highest treatment level of 2.3 x 1012 particles of the ethylene acrylic acid copolymer/ L in key pathways linked to central metabolism and energy reserves, oxidative stress, as well as ovulation and molting indicating a global transcriptomic response pattern. To put the results in perspective is challenging at this time, since, to date, microplastic environmental monitoring approaches have not been equipped to detect particles in the nano size range. However, the results of this study indicate that ethylene acrylic acid copolymer microplastics in the upper nano-size range are not expected to adversely affect D. magna growth, survival, or reproductive outcomes at concentrations up to 1012 particles/L.
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Project description:The transcriptome analysis by the human DNA microarray was applied to evaluate the impacts of whole wastewater effluents from the membrane bioreactors (MBRs) and the activated sludge process (AS), on the biological processes of human hepatoma HepG2 cells. The three conventional bioassays (i.e., cytotoxicity tests and bioluminescence inhibition test) and chemical analysis of the domestic effluent standards were conducted in parallel since they are well-established methods with previous applications to wastewater. A significant variation of effluent quality was sdemonstrated among the tested effluents despite that all effluents met the 40 national effluent standards. The three conventional bioassays supported the result of the transcriptome analysis, indicating the comparable or even higher sensitivity of the new assay. The most superior effluent quality was found in the MBR operated at a relatively long sludge retention time (i.e., 40 days) and small membrane pore size (i.e., 0.03 M-NM-<m). In addition, functional analysis of the differentially expressed genes revealed that the effluents made various impacts on the cellular functions, suggesting the transcriptome analysis by DNA microarray as more comprehensive, rapid and sensitive tool to detect multiple impacts of the whole effluents. Moreover, the potential genetic markers were proposed to quantitatively evaluate the treatability of the wastewater effluents. In this study, we examined the gene expression alteration in human hepatoma cell line, HepG2 exposed to the raw wastewater, effluents from three types of membrane bioreactors (MBRs), and the activated sludge process. Wastewater DNA microarray with 8795 human genes. MQ water was used as control. For duplicate, two dishes were prepared for each sample and individually treated in parallel.
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Project description:We investigated the impacts of wastewater effluent exposure on gene expression in adult fathead minnows, a freshwater fish commonly used as an ecotoxicological model.
2022-08-31 | GSE180719 | GEO
Project description:In this study, we exposed Caenorhabditis elegans wild types N2 to water collected from six sources in the Dutch village Sneek. The sources were: wastewater from a hospital, a community (80 households), a nursing home, influent into the local municipal wastewater treatment plant, effluent of the wastewater treatment plant, and surface water samples. The goal of the experiment was to determine if C. elegans can be used to identify pollutants in the water by transcriptional profiling. Age synchronized worms at developmental L4 larval stage were exposed to treatment for 24 hours. After flash freezing the samples, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.
2022-12-03 | E-MTAB-11260 | biostudies-arrayexpress
Project description:Disinfectant-resistant Serratia marcescens in a Hungarian hospital
| PRJEB65431 | ENA
Project description:The investigation about archaeological samples, which are of inestimable value, requires minimally destructive or nondestructive sampling techniques. One of the most promising and recent non-invasive techniques is known under the acronym EVA, an ethylene vinyl acetate film which avoids contamination and proteins damages. This paper reports the results of the first-ever analysis of proteins extracted from the EVA film applied to a tissue sample some 40000 years old. In particular, the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), via a shotgun MS-based approach was investigated. Proteomic and peptidomic analysis allowed the exploration of the mammoth dietary plants and its gut bacteria. The results were validated through the level of deamidation and other post-translational modifications of the peptides of the samples, which were used to discrimitate the “original” endogenous peptides from contaminant ones. Overall, the results of the metaproteomic analysis here reported are in accordance with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth.
2021-11-03 | PXD025518 | Pride